Here is a list of subsystems that people are working on.
| Cyanos Hierarchy |
| Level 1 | Level 2 | Level 3 | Level 4(Subsystem) | Author | Status* | Expertise level** | Forum Postings |
| Experimental Subsystems | | | | | | |
| | Essential gene lists | |
| Amino Acids and Derivatives | | | | | | |
| | Glutamine, glutamate, aspartate, asparagine; ammonia assimilation | | | | | |
| | | Ammonia assimilation | | | | |
| | | | ![[WWW]](/CyanoSEEDWiki/img/moin-www.gif "[WWW]") Ammonia assimilation | master:Ed | 2 | B |
| | | Glutamate | | | | |
| | | | Glutamate_biosynthesis | master:MattC | | |
| | | Aspartate and asparagine | | | | |
| | | | superpathway of glutamate, aspartate, asparagine biosynthisis | master:MattC | 4 | A |
| | Arginine; urea cycle, polyamines | | | | | |
| | | Arginine | | | | |
| | | | Arginine Biosynthesis | master:RickS | 2 | B |
| | | Polyamines | | | | |
| | | | Polyamine Metabolism | master:InesT_UCSD | 2 | B |
| | | | Putrescine and 4-aminobutyrate degradation | master:MikeK | 2 | B |
| | Proline and 4-hydroxyproline | | | | | |
| | | | Proline Synthesis | master:RickS | 2 | B |
| | Alanine, serine, and glycine | | | | | |
| | | Alanine | | | | |
| | | | Pyruvate Alanine Serine Interconversions | master:JasonS_UCSD | 2 | B |
| | | | Thermotoga Alanine Biosynthesis | master:rodionov | | |
| | | | Alanine Biosynthesis extended | master:AndreiO | | |
| | | Serine | | | | |
| | | | Serine synthesis | master:MikeK | 2 | B |
| | | | Serine Biosynthesis SA | master:SanjayA | | |
| | | Glycine | | | | |
| | | | Glycine_synthesis | master:MikeK | 2 | B |
| | Lysine, threonine, methionine, and cysteine | | | | | |
| | | Lysine | | | | |
| | | | Lysine_Biosynthesis_DAP_Pathway | master:AndreiO | 3 | P | Subsystem diagram |
| | | Threonine | | | | |
| | | | Threonine_synthesis | master:MikeK | 2 | B |
| | | | Threonine_to_Isoleucine | master:RossO | 3 | B |
| | | Methionine, formylmethionine and SAM | | | | |
| | | | Methionine Metabolism | master:MonicaM_UCSD | 2 | B |
| | | | Methionine Biosynthesis | master:rodionov | 3 | E |
| | | Cystein | | | | |
| | | | cysteine biosynthesis | master:RobE | 2 | B |
| | Branhed-chain amino acids | | | | | |
| | | Leucine | | | | |
| | | | Leucine_synthesis | master:MikeK | 2 | B |
| | | | Leucine_Degradation_and_HMG-CoA_Metabolism | master:VeronikaV | | | Subsystem diagram |
| | | | HMG CoA Synthesis | master:VeronikaV | | |
| | | Isoleucine | | | | |
| | | | Isoleucine Synthesis | master:BobO | 2 | B |
| | | Valine | | | | |
| | | | Valine_Synthesis | master:TerryD | 2 | B |
| | Aromatic amino acids and derivatives | | | | | |
| | | Shikimate, chorismate | | | | |
| | | | Chorismate Synthesis | master:VeronikaV | | |
| | | Phenylalanine | | | | |
| | | | Phenylalanine synthesis | master:MikeK | 2 | B |
| | | Tyrosine | | | | |
| | | | Tyrosine_synthesis | master:MikeK | 2 | B |
| | | Tryptophane | | | | |
| | | | Tryptophan Synthesis NMPDR | master:VeronikaV | 4 | A |
| | Histidine | | | | | |
| | | | Histidine Biosynthesis | master:RossO | 3 | A |
| | | | Histidine Degradation | master:RossO | 3 | A |
| Nitrogen Metabolism | | | | | | |
| | | | Ammonia assimilation | master:EdF | 2 | A |
| | | | Denitrification | master:rodionov | | |
| | | | Allantoin degradation | master:MattC | | |
| | | | Nitrate Assimilation | master:DanaH | 2 | B |
| | | | Nitrate and Nitrite Reduction | master:rodionov | 2 | B |
| | | | Nitrite Reduction | master:MattC | 2 | B |
| | | | Nitrosative stress | master:rodionov | 2 | B |
| | | | nitrogen fixation | master:FonsteinM | 1 | A |
| Sulfur Metabolism | | | | | | |
| | | | Sulfate assimilation | master:MattC | | |
| | | | Sulfur Metabolism | master:RobE | | |
| Phosphorus Metabolism | | | | | | |
| | | | P uptake (cyanobacteria) | master:acm@mit | | |
| Carbohydrates | | | | | | |
| | Central carbohydrate metabolism | | | | | |
| | | Glycolysis and gluconeogenesis | | | | |
| | | | Embden-Meyerhof and Gluconogenesis | master:RossO | 3 | A |
| | | | Archaeal Entner-Doudoroff Pathway | master:RossO | | |
| | | Pentose Phosphate Pathway | | | | |
| | | | Pentose phosphate pathway (SG) | master:SvetaG | 3 | A |
| | | Tricarboxylic acid cycle (TCA) | | | | |
| | | | TCA Cycle | master:RickS | 1 | B |
| | | | Glyoxylate Synthesis | master:RickS | 2 | B |
| | | | glyoxylate degradation | master:MattC | 2 | B |
| | | Pyruvate metabolism | | | | |
| | | | Pyruvate, PEP and Acetyl-CoA (anaplerotic reactions) | master:GaryH_UCSD | 2 | A |
| | | | Pyruvate Alanine Serine Interconversions | master:JasonS_UCSD | 2 | A |
| | | | Acetoin metabolism | master:MikeD_UCSD | 2 | A |
| | | Fermentation | | | | |
| | | | Heterofermentative lactate fermentation | master:MaryP_UCSD | 2 | A |
| | | | Homofermentative lactate fermentation | master:NeilJ_UCSD | 2 | A |
| | | | Acetogenesis from Pyruvate | master:LienC_UCSD | 2 | A |
| | | | Butyrate and Butanol Acetone fermentation | master:SouravB_UCSD | 2 | A |
| | CO2 fixation | | | | | |
| | | CO2 transport and concentration mechanisms | | | | |
| | | Calvin-Benson cycle | | | | |
| | | | Calvin-Benson cycle | master:SvetaG | 3 | A | Subsystem diagram |
| | | Reductive TCA cycle | | | | |
| | | Acetyl-CoA (Wood-Ljungdahl) pathway | | | | |
| | | Hydroxypropionate pathway | | | | |
| | Merthanogenesis | | | | | |
| | | | Methanogenesis | master:gjo | 3 | A |
| | One-carbon metabolism in methylotrophs | | | | | |
| | | | Methane metabolism | master:MikeR | | |
| | | Serine-isocitrate pathway | | | | |
| | | Ribulose-monophosphate pathway | | | | |
| | | Xylulose-monophosphate pathway | | | | |
| | Polysaccharide Metabolism | | | | | |
| | | Glycogen metabolism | | | | |
| | | Starch metabolism | | | | |
| | | Cellulose metabolism | | | | |
| | | Chitin metabolism | | | | |
| | Di- and oligosaccharides | | | | | |
| | | | Lactose degradation | master:MattC | 3 | B |
| | | | Sucrose Metabolism | master:NitinG_UCSD | | |
| | | | Trehalose biosynthesis | master:MattC | 4 | A |
| | Monosaccharides | | | | | |
| | | | D-arabinose degradation | master:MattC | | |
| | | | D-galactarate degradation | master:MattC | 2 | B |
| | | | D-glucarate degradation | master:MattC | 2 | B |
| | | | D-galacturonate degradation | master:MattC | 3 | B |
| | | | Galactose degradation | master:MattC | 3 | A |
| | | | Ketogluconate metabolism | master:MattC | 3 | B |
| | | | L-ascorbate degradation | master:MattC | 3 | A |
| | | | Mannose and fructose metabolism | master:HanYuC_UCSD | 2 | A |
| | | | mannose and GDP-mannose metabolism | master:MattC | 3 | A |
| | | | superpathway of fucose and rhamnose degradation | master:MattC | 3 | A |
| | Aminosugars | | | | | |
| | | | UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis | master:vasiliyP | 4 | A |
| | | | CMP-N-acetylneuraminate Biosynthesis | master:OlgaZ | 2 | A |
| | | | N-Acetyl-D-Glucosamine Utilization | master:OlgaZ | 4 | P | Subsystem diagram |
| | Sugar alcohols | | | | | |
| | | | Galactitol degradation | master:MattC | 4 | A |
| | | | Inositol catabolism by VV | master:VeronikaV | | |
| | | | superpathway of hexitol degradation | master:MattC | 3 | A |
| | Alkanes | | | | | |
| Fatty Acids and Lipids | | | | | | |
| | Glycerol | | | | | |
| | | | Glycerol Metabolism | master:MattC | 4 | A |
| | Fatty acids | | | | | |
| | | | Fatty Acid Biosynthesis FASII | master:AndreiO | 2 | P | Subsystem diagram |
| | | | carnitine metabolism | master:MattC | 4 | A |
| | | | fatty acid oxidation pathway | master:MattC | 2 | B |
| | Phospholipids | | | | | |
| | | | Sphingolipid biosynthesis | master:JorgeF | | |
| | | | Betaine biosynthesis | master:MattC | | |
| | Phosphoglycerides | | | | | |
| | | | Glycerolipid metabolism | master:VasiliyP_UCSD | | |
| Nucleosides and Nucleotides | | | | | | |
| | Purines | | | | | |
| | | | De Novo Purine Biosynthesis | master:RossO | 3 | A |
| | | | purine conversions | master:RossO | | |
| | | | purine conversions 2 | master:RossO | | |
| | Pyrimidines | | | | | |
| | | | De Novo Pyrimidine Synthesis | master:RossO | 3 | A |
| | | | pyrimidine conversions | master:RossO | | |
| | Ribonucleotide reduction | | | mater:rodionov | 3 | E |
| Cofactors, Vitamins, Prosthetic Groups, Pigments | | | | | | |
| | NAD and NADP | | | | | |
| | | | NAD and NADP cofactor biosynthesis global | master:AndreiO | 3 | E | Subsystem diagram |
| | Coenzyme A | | | | | |
| | | | Coenzyme A Biosynthesis | master:AndreiA | 4 | E | Subsystem diagram |
| | Coenzyme M | | | | | |
| | | | coenzyme M biosynthesis | master:AdamF | | |
| | Folate and pterines | | | | | |
| | | | Folate biosynthesis | master:vcrecy | | |
| | | | Pterin biosynthesis | master:vcrecy | | |
| | | | methanopterin biosynthesis | master:AdamF | | |
| | Iron-sulfur clusters | | | | | |
| | | | Fe-S cluster assembly | mater:rodionov | 3 | B |
| | Biotin | | | | | |
| | | | Biotin biosynthesis | mater:rodionov | | | Subsystem diagram |
| | | | Biotin-Dependent Transcarboxylation | master:AndreiO | | |
| | Riboflavin, FMN, FAD | | | | | |
| | | | Riboflavin metabolism | master:rodionov | 4 | E |
| | | | FMN and FAD biosynthesis | master:AndreiO | 4 | E | Subsystem diagram |
| | Thiamine and thiamin pyrophosphate | | | | | |
| | | | Thiamin biosynthesis | master:rodionov | 3 | E |
| | Pyridoxine | | | | | |
| | Lipoate and Lipoamide | | | | | |
| | Tocopherol | | | | | |
| | Quinone cofactors | | | | | |
| | | | Menaquinone Biosynthesis | master:RickS | | |
| | | | Menaquinone and Phylloquinone Biosynthesis | master:OlgaZ | 3 | A | Subsystem diagram |
| | Isoprenoids | | | | | |
| | | | Isoprenoid Biosynthesis | master:OlgaZ | 3 | P | Subsystem diagram |
| | | | polyisoprenoid biosynthesis | master:MattC | 2 | B |
| | | | Carotenoids | master:OlgaV | | | Subsystem diagram |
| | | | polyprenyl synthesis | master:NJ | | |
| | Tetrapyrroles | | | | | | Overview diagram |
| | | | Porphyrin, Heme, and Siroheme Biosynthesis | master:SvetaG | 3 | A |
| | | | Chlorophyll Biosynthesis | master:VeronikaV | 2 | A | Subsystem diargam |
| | | | Bilin Biosynthesis | master:OlgaZ | 3 | A |
| | Reductants | | | | | |
| | | | Glutathione Redox Metabolism | master:Neema_UCSD | | |
| | Siderophores | | | | | |
| | | | Enterobactin biosynthesis | master:MattC | 4 | A |
| Cell Wall and Capsule | | | | | | |
| | Peptidoglycan biosynthesis | | | | | |
| | | | Peptidoglycan Biosynthesis | master:RickS | 3 | A |
| | | | Peptidoglycan from UDP-N-acetylmuramate | master:vasiliyP | | | Subsystem diagram |
| | | | peptidoglycan synthesis | master:NJ | | |
| | Glycosylation | | | | | |
| | | | N-linked Glycosylation in Bacteria | master:OlgaZ | 2 | A |
| | Gram-Positive cell wall components | | | | | |
| | | Teichoic and teichuronic acids | | | | |
| | | S-layer | | | | |
| | | Neutral polysaccharides | | | | |
| | | Surface glycolipids | | | | |
| | | Surface lipoproteins | | | | |
| | | Surface proteins | | | | |
| | | Mycolic acid | | | | |
| | Gram-Negative cell wall components | | | | | |
| | | Lipid A | | | | |
| | | Core polysaccharide | | | | |
| | | O-specific polysaccharide | | | | |
| | | | dTDP-rhamnose synthesis | master:MikeK | 2 | B |
| | | Surface lipoproteins | | | | |
| | Archaeal cell wall | | | | | |
| | Capsular and extracellular polysacchrides | | | | | |
| Oxidative Phosphorylation | | | | | | |
| | Anaerobic respiratory chain | | | | | |
| | Aerobic respiratory chain | | | | | |
| | ATP synthases | | | | | |
| | | | F0F1-type ATP synthase | master:RickS | 3 | A |
| | | | V-Type ATP synthaase | master:RickS | 3 | A |
| | Soluble electron carries | | | | | |
| | Transhydrogenation | | | | | |
| | Protection from reactive oxygen species | | | | | |
| Photosynthesis | | | | | | |
| | Oxygenic photosynthesis | | | | | |
| | | | Photosystem I | master:Sveta | 2 | P |
| | | | Photosystem II | master:Sveta | 2 | P |
| | | | Cytochrome B6-F complex | master:Sveta | 2 | A |
| | | Soluble electron carries | | | | |
| | | Light harversting | | | | |
| | | | Phycobilisome | master:OlgaZ | 2 | A |
| | Anoxygenic photosynthesis | | | | | |
| | | Purple sulfur phototrophs | | | | |
| | | Purple nonsulfur phototrophs | | | | |
| | | Green nonsulfur phototrophs | | | | |
| | | Green sulfur phototrophs | | | | |
| | | Heliobacteria | | | | |
| Degradation/Utilization/Assimilation of Various Compounds | | | | | | |
| | | | Propionate Catabolism via 2-Methylcitrate Cycle | master:AndreiO | 1 | A | Subsystem diagram |
| | | | Tricarballylate Utilization | master:RossO | 2 | B |
| Miscellaneous | | | | | | |
| | | | Cyanophycin metabolism | master:MikeR | | |
| | | | ppGpp biosynthesis | master:MikeK | | |
| | | | Betaine biosynthesis | master:MattC | 3 | A |
| Secondary Metabolism | | | | | | |
| | Biosynthesis of Secondary Metabolites | | | | | |
| | Degradation of Xenobiotics | | | | | |
| DNA metabolism | | | | | | |
| | DNA Replication | | | | | |
| | DNA Modification | | | | | |
| | DNA Repair | | | | | |
| | | | DNA Repair Base Excision | master:MikeK | 2 | A |
| | DNA uptake, competence | | | | | |
| | | | gram plus late competence | master:alexS | | |
| | |
| RNA metabolism | | | | | | | | RNA polymerase I | master:gjo | 4 | E |
| | | | RNA polymerase II | master:gjo | 4 | E |
| | | | RNA polymerase III | master:gjo | 4 | E |
| | | | RNA polymerase II initiation factors | master:gjo | 4 | E |
| | | | RNA polymerase archaeal | master:gjo | 4 | E |
| | | | RNA polymerase bacterial | master:gjo | 4 | E |
| | | | archaeal general transcription factors | master:gjo | 4 | E |
| | | | tRNA aminoacylation | master:gjo | 4 | E |
| | | | tRNA processing | master:gjo | 4 | E |
| | | | tRNA splicing | master:gjo | 4 | E |
| | RNA processing and modification | | | | | |
| | | | Queuosine | master:vcrecy | 3 | A |
| | RNA degradation | | | | | |
| Protein Metabolism | | | | | | |
| | Protein Biosynthesis | | | | | |
| | | | Ribosome LSU bacterial | master:gjo | 4 | E |
| | | | Ribosome SSU bacterial | master:gjo | 4 | E |
| | | | Ribosome LSU eukaryotic and archaeal | master:gjo | 4 | E |
| | | | Ribosome SSU eukaryotic and archaeal | master:gjo | 4 | E |
| | | | tRNA aminoacylation | master:gjo | 4 | E |
| | Protein Degradation | | | | | |
| | | | archaeal proteasome | master:gjo | 4 | E |
| | | | Proteasome eukaryotic | master:gjo | 4 | E |
| | Protein Folding | | | | | |
| | | | Chaperones | master:MikeK | 2 | A |
| | | | GroEL GroES | master:MikeK | 2 | A |
| | Protein Processing and Modification | | | | | |
| | Protein Export and Secretion | | | | | |
| | | | General secretory pathway (Sec-SRP) complex (TC 3.A.5.1.1) | master:MattC | | |
| | | | Type II secretion system | master:MikeK | 2 | A |
| | | | Type III secretion system | master:MikeK | 2 | B |
| | | | Type IV secretion system | master:MikeK | 1 | A |
| Membrane Transport | | | | | | |
| | Channel/pore type transporters | | | | | |
| | Uni-, Sym- and Antiporters | | | | | |
| | Phosphotransferase Systems (PTS) | | | | | |
| | Transport ATPases | | | | | |
| | ABC transporters | | | | | |
| | | | ABC transporter alkylphosphonate (TC 3.A.1.9.1) | master:MattC | | |
| | | | ABC transporter arabinose (TC 3.A.1.2.2) | master:MattC | | |
| | | | ABC transporter branched-chain amino acid (TC 3.A.1.4.1) | master:MattC | | |
| | | | ABC transporter dipeptide (TC 3.A.1.5.2) | master:MattC | | |
| | | | ABC transporter ferric enterobactin (TC 3.A.1.14.2) | master:MattC | | |
| | | | ABC transporter ferrichrome (TC 3.A.1.14.3) | master:MattC | | |
| | | | ABC transporter galactose | master:MattC | | |
| | | | ABC transporter glutamate | master:MattC | | |
| | | | ABC transporter glutamine | master:MattC | | |
| | | | ABC transporter glycerol | master:MattC | | |
| | | | ABC transporter heme | master:MattC | | |
| | | | ABC transporter histidine | master:MattC | | |
| | | | ABC transporter iron(III) dicitrate | master:MattC | | |
| | | | ABC transporter leucine | master:MattC | | |
| | | | ABC transporter lysine arginine ornithine | master:MattC | | |
| | | | ABC transporter macrolide | master:MattC | | |
| | | | ABC transporter maltose | master:MattC | | |
| | | | ABC transporter molybdenum | master:MattC | | |
| | | | ABC transporter nickel | master:MattC | | |
| | | | ABC transporter oligopeptide | master:MattC | | |
| | | | Oligopeptide ABC transporters | master:SvetaG | | |
| | | | ABC transporter peptide | master:MattC | | |
| | | | ABC transporter phosphate | master:MattC | | |
| | | | ABC transporter polyamine putrescine spermidine (TC 3.A.1.11.1) | master:MattC | | |
| | | | ABC transporter potassium 3.A.3.7.1 | master:MattC | | |
| Cell Division and Cell Cycle | | | | | | |
| | | | Bacterial Cell Division | master:RickS | | |
| | | | Cyanobacterial Circadian Clock | master:OlgaZ | | |
| Motility and Chemotaxis | | | | | | |
| | | | Flagellum | master:RickS | | |
| Signal Transduction | | | | | | |
| Stress Response | | | | | | |
| VIRULENCE | | | |
| | Adhesion |
| | | | Fimbriae (Pili) |
| | | | Mannose-sensitive hemagglutinin type 4 pilus | RobE | 3 | A |
| | | | Afimbrial adhesins |
| |
| | Invasion | | | |
| | | | Listeria surface proteins: Internalin-like proteins | SvetaG | 2 | A |
| | | | Listeria surface proteins: LPXTG motif | SvetaG | 2 | A |
| | | | Invasins |
| | Growth in Macrophages |
| | | | superoxide dismutases |
| | | | Macrophage induced proteins |
| | Toxins |
| | | | Cytolethal distending toxin of Campylobacter jejuni | OlgaZ | 4 | A |
| | Superantigens |
| | Specific Enzymes |
| | | | Staphylococcal enterotoxin (e.g PMID:12704169) |
| | Matrix binding proteins |
| | Resistance to Antibiotics | |
| | | | Beta-lactam | MikeK | 1 | B | |
| | | | Glycopeptides | |
| | | | Aminoglycosides | |
| | | | Tetracyclines | |
| | | | Macrolides | |
| | | | Lincosamides | |
| | | | Oxazolidinones | |
| | | | Fluoroquinolones | MattC | 1 | B | fourum posting |
| | | | Rifampin | |
| | | | Trimethoprim | |
| | | | Mupirocin | |
| | Nutrient Acquisition in Host | |
| | | | Iron Acquisition Mechanisms |
| | Virulence Islands, Prophages | | | |
| | | | Listeria Pathogenicity Island LIPI-1 | SvetaG | 2 | A | |
| | | | Listeria Pathogenicity Island LIPI-1 extended | SvetaG | 2 | A | |
| Plasmids, Transposable Elements, Viruses, and Phages | | | | | | |
| | Replication | | | | | |
| | Packaging | | | | | |
| | Cell lysis | | | | | |
| | Lysogeny | | | | | |
| | Morons | | | | | |
| | Transposition | | | | | |
